Project name: 4AJY_L129P [mutate: LP129V]

Status: done

Started: 2020-09-18 14:56:00
Settings
Chain sequence(s) V: RPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIA
input PDB
Selected Chain(s) V
Distance of aggregation 10 Å
FoldX usage Yes
Dynamic mode Yes
Automated mutations No
Mutated residues LP129V
Energy difference between WT (input) and mutated protein (by FoldX) 3.50612 kcal/mol

CAUTION: Your mutation/s can destabilize the protein structure
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:00)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:00)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with V chain(s) selected             (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:00)
[INFO]       FoldX:    Building mutant model                                                       (00:01:40)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:01:43)
[INFO]       CABS:     Running CABS flex simulation                                                (00:02:33)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:25:02)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:25:03)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:25:03)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:25:04)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:25:05)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:25:05)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:25:06)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:25:07)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:25:07)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:25:09)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:25:09)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:25:10)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:25:11)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:25:13)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:25:13)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:25:13)
[INFO]       Main:     Simulation completed successfully.                                          (00:25:17)
Show buried residues
Minimal score value
-4.2241
Maximal score value
2.0894
Average score
-0.6619
Total score value
-97.9541
Download the table (csv)

The table below lists A3D score for protein residues. Residues with A3D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan3D score mutation
residue index residue name chain Aggrescan3D score
mutation
60 R V -1.8843
61 P V -1.3470
62 V V -0.7447
63 L V -0.8286
64 R V -0.3558
65 S V 0.2831
66 V V 1.1270
67 N V -0.0049
68 S V -1.1879
69 R V -2.6508
70 E V -2.2904
71 P V -1.9959
72 S V 0.0000
73 Q V -1.3908
74 V V 0.0000
75 I V -0.1287
76 F V 0.0000
77 C V -0.1132
78 N V 0.0000
79 R V -0.1887
80 S V -0.3004
81 P V -0.2528
82 R V 0.0000
83 V V 1.1173
84 V V 0.0000
85 L V 0.8837
86 P V 0.0000
87 V V 0.0000
88 W V 0.0000
89 L V 0.5871
90 N V 0.0000
91 F V 1.3311
92 D V -0.6438
93 G V -0.9272
94 E V -0.7278
95 P V -0.3199
96 Q V -0.6675
97 P V -0.2188
98 Y V 0.2064
99 P V 0.2283
100 T V 0.3971
101 L V 0.0000
102 P V -0.1019
103 P V -0.4081
104 G V -0.6926
105 T V -0.8993
106 G V -1.3595
107 R V -2.0165
108 R V -2.4363
109 I V 0.0000
110 H V -1.1789
111 S V 0.0000
112 Y V -1.3759
113 R V -1.5192
114 G V 0.0000
115 H V 0.0000
116 L V 0.0000
117 W V 0.0000
118 L V 0.0000
119 F V 0.0000
120 R V 0.1005
121 D V 0.0000
122 A V 0.2549
123 G V -0.1129
124 T V 0.0029
125 H V -0.0082
126 D V 0.0000
127 G V 0.0000
128 L V 0.0000
129 P V -0.5260 mutated: LP129V
130 V V 0.0000
131 N V -1.7687
132 Q V -1.9115
133 T V -1.2240
134 E V -0.9387
135 L V 0.0000
136 F V 0.0000
137 V V 0.4165
138 P V 0.2311
139 S V -0.2674
140 L V -0.5551
141 N V -2.0468
142 V V -1.7958
143 D V -2.5023
144 G V -1.9860
145 Q V -1.7728
146 P V -0.6533
147 I V 1.1174
148 F V 1.8567
149 A V 0.0000
150 N V -0.6381
151 I V 0.0000
152 T V 0.0610
153 L V 0.8844
154 P V 1.3671
155 V V 2.0894
156 Y V 1.0622
157 T V 0.6811
158 L V 1.1747
159 K V -0.6233
160 E V -0.7188
161 R V 0.1736
162 C V 0.1137
163 L V 0.0000
164 Q V 0.0000
165 V V 0.6753
166 V V 0.5136
167 R V 0.0000
168 S V 0.4002
169 L V 1.3170
170 V V -0.5231
171 K V -2.4160
172 P V -2.6772
173 E V -3.7291
174 N V -2.9828
175 Y V 0.0000
176 R V -4.2241
177 R V -3.5235
178 L V -1.6672
179 D V -1.7254
180 I V 0.0674
181 V V 0.6358
182 R V -1.8148
183 S V -1.1674
184 L V 0.0000
185 Y V -2.3192
186 E V -3.3442
187 D V -2.7887
188 L V 0.0000
189 E V -3.3071
190 D V -3.4256
191 H V -2.3317
192 P V -2.0076
193 N V -1.6857
194 V V -1.1273
195 Q V -1.9552
196 K V -2.4155
197 D V 0.0000
198 L V 0.0000
199 E V -2.8919
200 R V -2.9711
201 L V 0.0000
202 T V -2.2129
203 Q V -2.5596
204 E V -2.6786
205 R V -2.1560
206 I V 0.5010
207 A V 0.0236
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View in 3Dmol
Play the video

CABS-flex predictions of flexibility of input structure

In dynamic mode, A3D analysis is performed on the set of models reflecting fluctuations of the input structure (predicted by CABS-flex method, models are numbered from 0 to 11) and the input model. Their A3D scores are provided below in the table.
The right panel presents comparison of the most aggregation prone model (with the highest A3D score, -0.6619 in this case) with the input model (the most aggregation prone model in blue, input in red) and RMSF plot which shows the extent of residue fluctuations in Angstroms (predicted by CABS-flex).

Model
Average A3D Score
model_8 -0.6619 View CSV PDB
model_11 -0.7173 View CSV PDB
model_6 -0.7707 View CSV PDB
model_0 -0.7733 View CSV PDB
model_2 -0.796 View CSV PDB
input -0.7994 View CSV PDB
model_9 -0.8153 View CSV PDB
model_7 -0.8157 View CSV PDB
model_5 -0.8272 View CSV PDB
model_10 -0.8745 View CSV PDB
model_4 -0.9189 View CSV PDB
model_1 -0.9337 View CSV PDB
model_3 -0.9421 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018